Starting phenix.real_space_refine on Sun Oct 13 01:11:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfy_43194/10_2024/8vfy_43194.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfy_43194/10_2024/8vfy_43194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfy_43194/10_2024/8vfy_43194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfy_43194/10_2024/8vfy_43194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfy_43194/10_2024/8vfy_43194.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfy_43194/10_2024/8vfy_43194.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 342 5.49 5 S 21 5.16 5 C 7786 2.51 5 N 2611 2.21 5 O 3286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14046 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Time building chain proxies: 8.05, per 1000 atoms: 0.57 Number of scatterers: 14046 At special positions: 0 Unit cell: (84.48, 118.8, 192.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 342 15.00 O 3286 8.00 N 2611 7.00 C 7786 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 68.1% alpha, 3.2% beta 171 base pairs and 306 stacking pairs defined. Time for finding SS restraints: 6.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.742A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.549A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.537A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.809A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.637A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.507A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.527A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.561A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.690A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 4.029A pdb=" N TRP O 214 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.804A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.521A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.486A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.723A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.520A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.468A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231 436 hydrogen bonds defined for protein. 1278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 306 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2566 1.33 - 1.45: 4879 1.45 - 1.57: 6846 1.57 - 1.69: 682 1.69 - 1.81: 35 Bond restraints: 15008 Sorted by residual: bond pdb=" N HIS O 168 " pdb=" CA HIS O 168 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N LYS D 30 " pdb=" CA LYS D 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ALA C 10 " pdb=" CA ALA C 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N LYS H 30 " pdb=" CA LYS H 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 15003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 20049 1.17 - 2.33: 1297 2.33 - 3.50: 345 3.50 - 4.66: 34 4.66 - 5.83: 6 Bond angle restraints: 21731 Sorted by residual: angle pdb=" C2' DT J 55 " pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 113.50 117.99 -4.49 1.50e+00 4.44e-01 8.98e+00 angle pdb=" C2' DT I 140 " pdb=" C1' DT I 140 " pdb=" N1 DT I 140 " ideal model delta sigma weight residual 113.50 117.92 -4.42 1.50e+00 4.44e-01 8.69e+00 angle pdb=" C2' DC I 110 " pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 113.50 117.76 -4.26 1.50e+00 4.44e-01 8.07e+00 angle pdb=" C2' DT I 161 " pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 113.50 117.59 -4.09 1.50e+00 4.44e-01 7.43e+00 angle pdb=" C2' DT I 69 " pdb=" C1' DT I 69 " pdb=" N1 DT I 69 " ideal model delta sigma weight residual 113.50 117.55 -4.05 1.50e+00 4.44e-01 7.29e+00 ... (remaining 21726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 6504 31.36 - 62.73: 1665 62.73 - 94.09: 52 94.09 - 125.46: 0 125.46 - 156.82: 2 Dihedral angle restraints: 8223 sinusoidal: 5666 harmonic: 2557 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 63.18 156.82 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 68.58 151.42 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA LYS O 237 " pdb=" C LYS O 237 " pdb=" N PRO O 238 " pdb=" CA PRO O 238 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 8220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1616 0.032 - 0.064: 525 0.064 - 0.095: 263 0.095 - 0.127: 38 0.127 - 0.159: 5 Chirality restraints: 2447 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2444 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO O 238 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 140 " 0.038 2.00e-02 2.50e+03 1.78e-02 7.88e+00 pdb=" N1 DT I 140 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 140 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT I 140 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 140 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DT I 140 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I 140 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT I 140 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 140 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 140 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO O 171 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO O 172 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO O 172 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO O 172 " 0.027 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1294 2.74 - 3.28: 12610 3.28 - 3.82: 27731 3.82 - 4.36: 32977 4.36 - 4.90: 47101 Nonbonded interactions: 121713 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.203 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 72 " pdb=" OE2 GLU D 76 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR F 72 " pdb=" OE2 GLU H 76 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.275 3.040 ... (remaining 121708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 36.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15008 Z= 0.254 Angle : 0.678 5.829 21731 Z= 0.427 Chirality : 0.039 0.159 2447 Planarity : 0.005 0.073 1565 Dihedral : 26.421 156.825 6575 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.74 % Favored : 98.15 % Rotamer: Outliers : 0.27 % Allowed : 1.21 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.29), residues: 863 helix: 2.21 (0.22), residues: 577 sheet: -1.65 (1.37), residues: 12 loop : -0.34 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.007 0.001 PHE E 104 TYR 0.007 0.001 TYR G 57 ARG 0.003 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8872 (p) cc_final: 0.8313 (t) REVERT: A 76 GLN cc_start: 0.8172 (mt0) cc_final: 0.7704 (mt0) REVERT: B 85 ASP cc_start: 0.9143 (m-30) cc_final: 0.8911 (m-30) REVERT: C 90 ASP cc_start: 0.8325 (t0) cc_final: 0.8071 (t0) REVERT: C 95 LYS cc_start: 0.9288 (ttpt) cc_final: 0.9063 (tttm) REVERT: D 108 LYS cc_start: 0.8240 (ptmm) cc_final: 0.8016 (ptpp) REVERT: E 79 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8520 (mtpm) REVERT: G 120 THR cc_start: 0.8473 (p) cc_final: 0.8052 (p) REVERT: H 59 MET cc_start: 0.9127 (tpp) cc_final: 0.8898 (tpt) REVERT: H 113 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8341 (tt0) REVERT: H 115 THR cc_start: 0.9240 (m) cc_final: 0.9030 (p) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 1.8300 time to fit residues: 362.1718 Evaluate side-chains 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 47 GLN E 68 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15008 Z= 0.254 Angle : 0.615 6.564 21731 Z= 0.370 Chirality : 0.036 0.143 2447 Planarity : 0.005 0.076 1565 Dihedral : 30.323 150.403 4803 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 2.43 % Allowed : 13.09 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.28), residues: 863 helix: 2.25 (0.21), residues: 589 sheet: -1.54 (1.35), residues: 12 loop : -0.06 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.012 0.001 PHE O 254 TYR 0.014 0.001 TYR H 40 ARG 0.007 0.001 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8785 (p) cc_final: 0.8288 (t) REVERT: A 76 GLN cc_start: 0.8063 (mt0) cc_final: 0.7548 (mt0) REVERT: B 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8971 (m-30) REVERT: C 13 LYS cc_start: 0.9181 (tppp) cc_final: 0.8881 (tppp) REVERT: C 90 ASP cc_start: 0.8151 (t0) cc_final: 0.7879 (t0) REVERT: C 91 GLU cc_start: 0.7725 (tp30) cc_final: 0.7504 (tp30) REVERT: C 95 LYS cc_start: 0.9209 (ttpt) cc_final: 0.9002 (ttmt) REVERT: D 63 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: D 108 LYS cc_start: 0.8232 (ptmm) cc_final: 0.7948 (ptpp) REVERT: D 119 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8165 (p) REVERT: E 77 ASP cc_start: 0.8859 (m-30) cc_final: 0.8651 (t0) REVERT: G 90 ASP cc_start: 0.8620 (t70) cc_final: 0.8314 (t0) REVERT: H 59 MET cc_start: 0.9199 (tpp) cc_final: 0.8894 (tpt) REVERT: H 113 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8368 (tt0) REVERT: O 190 MET cc_start: 0.6373 (ttp) cc_final: 0.5695 (tpp) outliers start: 18 outliers final: 10 residues processed: 136 average time/residue: 1.8362 time to fit residues: 266.6815 Evaluate side-chains 122 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.0070 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 38 ASN G 104 GLN H 49 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15008 Z= 0.253 Angle : 0.607 9.424 21731 Z= 0.364 Chirality : 0.035 0.129 2447 Planarity : 0.005 0.077 1565 Dihedral : 30.415 149.502 4803 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 1.89 % Allowed : 15.11 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.28), residues: 863 helix: 2.28 (0.21), residues: 588 sheet: -1.46 (1.35), residues: 12 loop : 0.06 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 199 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.017 0.002 TYR O 197 ARG 0.006 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8023 (mt0) cc_final: 0.7443 (mt0) REVERT: B 85 ASP cc_start: 0.9235 (m-30) cc_final: 0.8995 (m-30) REVERT: C 90 ASP cc_start: 0.8116 (t0) cc_final: 0.7850 (t0) REVERT: C 91 GLU cc_start: 0.7749 (tp30) cc_final: 0.7426 (tm-30) REVERT: C 95 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8931 (ttmt) REVERT: D 57 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8912 (mtpt) REVERT: D 63 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8266 (m-40) REVERT: D 71 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: D 108 LYS cc_start: 0.8285 (ptmm) cc_final: 0.8003 (ptpp) REVERT: E 63 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7835 (mmm160) REVERT: F 24 ASP cc_start: 0.8202 (t0) cc_final: 0.7973 (t0) REVERT: G 90 ASP cc_start: 0.8496 (t70) cc_final: 0.8211 (t0) REVERT: G 119 LYS cc_start: 0.8617 (mptt) cc_final: 0.8397 (mmtt) REVERT: H 31 ARG cc_start: 0.8348 (pmt170) cc_final: 0.7812 (ptt90) REVERT: H 113 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8369 (tt0) REVERT: O 190 MET cc_start: 0.6321 (ttp) cc_final: 0.5939 (tpp) outliers start: 14 outliers final: 7 residues processed: 128 average time/residue: 1.9525 time to fit residues: 266.4554 Evaluate side-chains 124 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15008 Z= 0.215 Angle : 0.594 8.658 21731 Z= 0.356 Chirality : 0.034 0.130 2447 Planarity : 0.004 0.078 1565 Dihedral : 30.394 148.984 4803 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.57 % Rotamer: Outliers : 2.16 % Allowed : 15.11 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.28), residues: 863 helix: 2.33 (0.21), residues: 589 sheet: -1.17 (1.37), residues: 12 loop : 0.04 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 199 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.001 PHE E 67 TYR 0.014 0.001 TYR B 88 ARG 0.006 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8588 (p) cc_final: 0.8339 (p) REVERT: B 85 ASP cc_start: 0.9224 (m-30) cc_final: 0.9009 (m-30) REVERT: C 90 ASP cc_start: 0.8119 (t0) cc_final: 0.7868 (t0) REVERT: C 91 GLU cc_start: 0.7755 (tp30) cc_final: 0.7340 (tm-30) REVERT: C 95 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8758 (ttmp) REVERT: D 63 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8230 (m-40) REVERT: D 71 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: D 108 LYS cc_start: 0.8161 (ptmm) cc_final: 0.7836 (ptpp) REVERT: G 90 ASP cc_start: 0.8283 (t70) cc_final: 0.7978 (t0) REVERT: H 31 ARG cc_start: 0.8369 (pmt170) cc_final: 0.7827 (ptt90) REVERT: H 76 GLU cc_start: 0.9141 (tp30) cc_final: 0.8918 (mm-30) REVERT: H 101 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8743 (mm) REVERT: O 190 MET cc_start: 0.6334 (ttp) cc_final: 0.5769 (tpp) outliers start: 16 outliers final: 6 residues processed: 137 average time/residue: 1.7647 time to fit residues: 258.4918 Evaluate side-chains 120 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 113 HIS B 25 ASN C 38 ASN H 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15008 Z= 0.366 Angle : 0.657 7.620 21731 Z= 0.387 Chirality : 0.038 0.138 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.895 151.651 4803 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 2.56 % Allowed : 17.14 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.28), residues: 863 helix: 2.07 (0.21), residues: 588 sheet: -1.12 (1.36), residues: 12 loop : -0.14 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP O 199 HIS 0.007 0.001 HIS F 75 PHE 0.008 0.001 PHE O 228 TYR 0.022 0.002 TYR B 88 ARG 0.007 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8186 (t0) cc_final: 0.7901 (t0) REVERT: C 91 GLU cc_start: 0.7812 (tp30) cc_final: 0.7505 (tm-30) REVERT: C 95 LYS cc_start: 0.9162 (ttpt) cc_final: 0.8923 (ttmt) REVERT: D 63 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8229 (m-40) REVERT: D 71 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: D 108 LYS cc_start: 0.8367 (ptmm) cc_final: 0.8069 (ptpp) REVERT: E 63 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7605 (mmp80) REVERT: G 90 ASP cc_start: 0.8385 (t70) cc_final: 0.8117 (t0) REVERT: H 31 ARG cc_start: 0.8295 (pmt170) cc_final: 0.7858 (ptt90) REVERT: H 76 GLU cc_start: 0.9198 (tp30) cc_final: 0.8923 (mm-30) REVERT: O 190 MET cc_start: 0.6206 (ttp) cc_final: 0.5726 (tpp) outliers start: 19 outliers final: 10 residues processed: 129 average time/residue: 1.8171 time to fit residues: 250.5840 Evaluate side-chains 123 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 0.0870 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 25 ASN C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15008 Z= 0.195 Angle : 0.616 10.237 21731 Z= 0.364 Chirality : 0.035 0.235 2447 Planarity : 0.005 0.080 1565 Dihedral : 30.755 149.502 4803 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 1.62 % Allowed : 18.76 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.28), residues: 863 helix: 2.17 (0.21), residues: 589 sheet: -1.08 (1.39), residues: 12 loop : 0.07 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 199 HIS 0.001 0.000 HIS H 49 PHE 0.013 0.001 PHE E 67 TYR 0.032 0.002 TYR B 88 ARG 0.007 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8110 (t0) cc_final: 0.7824 (t0) REVERT: C 91 GLU cc_start: 0.7742 (tp30) cc_final: 0.7524 (tm-30) REVERT: C 95 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8864 (ttmt) REVERT: D 63 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: D 71 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: D 108 LYS cc_start: 0.8246 (ptmm) cc_final: 0.7938 (ptpp) REVERT: D 113 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: G 90 ASP cc_start: 0.8347 (t70) cc_final: 0.8037 (t0) REVERT: H 40 TYR cc_start: 0.8695 (m-80) cc_final: 0.8310 (m-80) REVERT: H 76 GLU cc_start: 0.9188 (tp30) cc_final: 0.8954 (mm-30) REVERT: O 190 MET cc_start: 0.6117 (ttp) cc_final: 0.5706 (tpp) outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 1.7650 time to fit residues: 247.4415 Evaluate side-chains 125 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 196 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15008 Z= 0.241 Angle : 0.609 8.065 21731 Z= 0.363 Chirality : 0.035 0.134 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.663 149.659 4803 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 1.89 % Allowed : 20.24 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.28), residues: 863 helix: 2.20 (0.21), residues: 589 sheet: -1.14 (1.40), residues: 12 loop : 0.05 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 199 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.027 0.001 TYR B 88 ARG 0.007 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.9172 (tppp) cc_final: 0.8874 (tppp) REVERT: C 50 TYR cc_start: 0.9165 (t80) cc_final: 0.8957 (t80) REVERT: C 90 ASP cc_start: 0.8093 (t0) cc_final: 0.7857 (t0) REVERT: C 91 GLU cc_start: 0.7767 (tp30) cc_final: 0.7508 (tm-30) REVERT: C 95 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8892 (ttmt) REVERT: D 63 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8222 (m-40) REVERT: D 71 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: D 108 LYS cc_start: 0.8210 (ptmm) cc_final: 0.7881 (ptpp) REVERT: G 90 ASP cc_start: 0.8359 (t70) cc_final: 0.8060 (t0) REVERT: G 116 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8771 (mt) REVERT: H 76 GLU cc_start: 0.9174 (tp30) cc_final: 0.8933 (mm-30) REVERT: H 113 GLU cc_start: 0.8538 (tt0) cc_final: 0.8170 (tm-30) REVERT: O 190 MET cc_start: 0.6054 (ttp) cc_final: 0.5557 (tpp) outliers start: 14 outliers final: 7 residues processed: 131 average time/residue: 1.8601 time to fit residues: 259.9116 Evaluate side-chains 125 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15008 Z= 0.197 Angle : 0.615 10.393 21731 Z= 0.363 Chirality : 0.034 0.167 2447 Planarity : 0.005 0.080 1565 Dihedral : 30.624 149.245 4803 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 1.48 % Allowed : 21.05 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.28), residues: 863 helix: 2.26 (0.21), residues: 589 sheet: -1.15 (1.40), residues: 12 loop : 0.08 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 199 HIS 0.002 0.000 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.038 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.9210 (tppp) cc_final: 0.8920 (tppp) REVERT: C 50 TYR cc_start: 0.9124 (t80) cc_final: 0.8884 (t80) REVERT: C 90 ASP cc_start: 0.8058 (t0) cc_final: 0.7817 (t0) REVERT: C 91 GLU cc_start: 0.7728 (tp30) cc_final: 0.7483 (tm-30) REVERT: C 95 LYS cc_start: 0.9119 (ttpt) cc_final: 0.8898 (ttmt) REVERT: D 63 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8210 (m-40) REVERT: D 71 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: D 108 LYS cc_start: 0.8188 (ptmm) cc_final: 0.7857 (ptpp) REVERT: G 90 ASP cc_start: 0.8338 (t70) cc_final: 0.8032 (t0) REVERT: G 116 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8730 (mt) REVERT: H 40 TYR cc_start: 0.8682 (m-80) cc_final: 0.8254 (m-80) REVERT: H 76 GLU cc_start: 0.9174 (tp30) cc_final: 0.8942 (mm-30) REVERT: H 113 GLU cc_start: 0.8503 (tt0) cc_final: 0.8268 (mt-10) REVERT: H 115 THR cc_start: 0.9288 (m) cc_final: 0.9052 (p) REVERT: O 190 MET cc_start: 0.6019 (ttp) cc_final: 0.5344 (tpp) REVERT: O 215 GLN cc_start: 0.7506 (pp30) cc_final: 0.7224 (pp30) outliers start: 11 outliers final: 7 residues processed: 129 average time/residue: 1.7495 time to fit residues: 241.3188 Evaluate side-chains 130 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 112 optimal weight: 0.0470 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN H 63 ASN O 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15008 Z= 0.243 Angle : 0.619 8.733 21731 Z= 0.366 Chirality : 0.035 0.146 2447 Planarity : 0.005 0.080 1565 Dihedral : 30.629 149.619 4803 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.20 % Favored : 97.68 % Rotamer: Outliers : 2.02 % Allowed : 20.92 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.28), residues: 863 helix: 2.23 (0.21), residues: 590 sheet: -1.02 (1.41), residues: 12 loop : 0.05 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 214 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.035 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7773 (tp30) cc_final: 0.7497 (mm-30) REVERT: C 90 ASP cc_start: 0.8052 (t0) cc_final: 0.7817 (t0) REVERT: C 91 GLU cc_start: 0.7763 (tp30) cc_final: 0.7533 (tm-30) REVERT: D 63 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8275 (m-40) REVERT: D 71 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: D 108 LYS cc_start: 0.8343 (ptmm) cc_final: 0.8036 (ptpp) REVERT: G 90 ASP cc_start: 0.8378 (t70) cc_final: 0.8076 (t0) REVERT: G 116 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8750 (mt) REVERT: H 31 ARG cc_start: 0.8248 (pmt170) cc_final: 0.7625 (ttp-170) REVERT: H 76 GLU cc_start: 0.9169 (tp30) cc_final: 0.8947 (mm-30) REVERT: H 113 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: O 190 MET cc_start: 0.5941 (ttp) cc_final: 0.5564 (tpp) REVERT: O 215 GLN cc_start: 0.7283 (pp30) cc_final: 0.7009 (pp30) REVERT: O 253 MET cc_start: 0.5004 (tpt) cc_final: 0.1382 (mtt) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 1.8359 time to fit residues: 249.0250 Evaluate side-chains 129 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 108 optimal weight: 40.0000 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15008 Z= 0.272 Angle : 0.640 10.730 21731 Z= 0.373 Chirality : 0.035 0.157 2447 Planarity : 0.005 0.079 1565 Dihedral : 30.703 150.333 4803 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Rotamer: Outliers : 1.75 % Allowed : 21.05 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.28), residues: 863 helix: 2.17 (0.21), residues: 590 sheet: -0.78 (1.45), residues: 12 loop : 0.02 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 214 HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.042 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.8622 (p) cc_final: 0.7982 (t) REVERT: C 90 ASP cc_start: 0.8078 (t0) cc_final: 0.7833 (t0) REVERT: D 59 MET cc_start: 0.9095 (tpt) cc_final: 0.8519 (mmm) REVERT: D 63 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8264 (m-40) REVERT: D 71 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: D 108 LYS cc_start: 0.8349 (ptmm) cc_final: 0.8041 (ptpp) REVERT: G 90 ASP cc_start: 0.8375 (t70) cc_final: 0.8054 (t0) REVERT: G 116 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8774 (mt) REVERT: H 31 ARG cc_start: 0.8326 (pmt170) cc_final: 0.7655 (ttp-170) REVERT: H 40 TYR cc_start: 0.8755 (m-80) cc_final: 0.8341 (m-80) REVERT: H 76 GLU cc_start: 0.9191 (tp30) cc_final: 0.8953 (mm-30) REVERT: H 113 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: O 190 MET cc_start: 0.6139 (ttp) cc_final: 0.5865 (tpp) REVERT: O 215 GLN cc_start: 0.7253 (pp30) cc_final: 0.6994 (pp30) REVERT: O 253 MET cc_start: 0.5153 (tpt) cc_final: 0.1477 (mtt) outliers start: 13 outliers final: 9 residues processed: 123 average time/residue: 2.0082 time to fit residues: 263.6926 Evaluate side-chains 130 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 220 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.105940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070211 restraints weight = 35442.130| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.03 r_work: 0.3134 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15008 Z= 0.225 Angle : 0.641 11.312 21731 Z= 0.372 Chirality : 0.035 0.172 2447 Planarity : 0.004 0.080 1565 Dihedral : 30.647 149.543 4803 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 21.73 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.28), residues: 863 helix: 2.21 (0.21), residues: 589 sheet: -0.72 (1.46), residues: 12 loop : 0.05 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 199 HIS 0.002 0.000 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.048 0.002 TYR B 88 ARG 0.008 0.000 ARG H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4632.27 seconds wall clock time: 83 minutes 37.72 seconds (5017.72 seconds total)